Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1237
  Reference Plasmid   NZ_CP140112.1
  Reference Plasmid Size   518222
  Reference Plasmid GC Content   0.57
  Reference Plasmid Mobility Type   non-mobilizable





Mutation sites in the plasmid cluster


The table lists mutations identified in the plasmid cluster.
Note: Mutations identified in this plasmid cluster are listed below. Click on a mutation ID to view full details..

mutid gname pos count tissue frequnt biotype consequence impact nucchange aachange
M0115018 PNLAMIBE_00354 264535 7 Skin 0.11 protein_coding missense_variant MODERATE 491C>T Ala164Val
M0115019 PNLAMIBE_00276 198815 14 Skin 0.23 protein_coding synonymous_variant LOW 1074C>T Ser358Ser
M0115020 PNLAMIBE_00346 254984 6 Skin 0.10 protein_coding missense_variant MODERATE 677A>G Asp226Gly
M0115021 PNLAMIBE_00350 260532 6 Skin 0.10 protein_coding missense_variant MODERATE 182A>G His61Arg
M0115022 PNLAMIBE_00348 262450 6 Skin 0.10 protein_coding upstream_gene_variant MODIFIER -3918G>T None
M0115023 PNLAMIBE_00277 199432 4 Skin 0.07 protein_coding missense_variant MODERATE 6C>A Asp2Glu
M0115024 PNLAMIBE_00278 200517 3 Skin 0.05 protein_coding synonymous_variant LOW 186T>C Leu62Leu
M0115025 PNLAMIBE_00278 200532 3 Skin 0.05 protein_coding synonymous_variant LOW 201C>T Gly67Gly
M0115026 PNLAMIBE_00278 200538 3 Skin 0.05 protein_coding synonymous_variant LOW 207A>G Glu69Glu
M0115027 PNLAMIBE_00278 200542 3 Skin 0.05 protein_coding missense_variant MODERATE 211A>G Asn71Asp
M0115028 PNLAMIBE_00278 200544 3 Skin 0.05 protein_coding synonymous_variant LOW 213C>T Asn71Asn
M0115029 PNLAMIBE_00278 200553 3 Skin 0.05 protein_coding synonymous_variant LOW 222T>C Arg74Arg
M0115030 PNLAMIBE_00278 200562 3 Skin 0.05 protein_coding synonymous_variant LOW 231C>T Ser77Ser
M0115031 PNLAMIBE_00278 200565 4 Skin 0.07 protein_coding synonymous_variant LOW 234T>C Phe78Phe
M0115032 PNLAMIBE_00278 200615 3 Skin 0.05 protein_coding missense_variant MODERATE 284A>C Asp95Ala
M0115033 PNLAMIBE_00278 200616 4 Skin 0.07 protein_coding synonymous_variant LOW 285T>C Asp95Asp
M0115034 PNLAMIBE_00278 200625 4 Skin 0.07 protein_coding synonymous_variant LOW 294G>A Glu98Glu
M0115035 PNLAMIBE_00278 200649 3 Skin 0.05 protein_coding synonymous_variant LOW 318G>A Val106Val
M0115036 PNLAMIBE_00278 200650 3 Skin 0.05 protein_coding synonymous_variant LOW 319T>C Leu107Leu
M0115037 PNLAMIBE_00278 200660 4 Skin 0.07 protein_coding missense_variant MODERATE 329C>G Thr110Arg
M0115038 PNLAMIBE_00278 200663 4 Skin 0.07 protein_coding missense_variant MODERATE 332A>T His111Leu
M0115039 PNLAMIBE_00278 200671 3 Skin 0.05 protein_coding missense_variant MODERATE 340A>C Lys114Gln
M0115040 PNLAMIBE_00276 198848 3 Skin 0.05 protein_coding synonymous_variant LOW 1107G>A Ala369Ala
M0115041 PNLAMIBE_00276 198864 3 Skin 0.05 protein_coding missense_variant MODERATE 1123A>G Ile375Val
M0115042 PNLAMIBE_00276 198867 3 Skin 0.05 protein_coding missense_variant MODERATE 1126A>G Thr376Ala
M0115043 PNLAMIBE_00276 198872 3 Skin 0.05 protein_coding synonymous_variant LOW 1131G>T Arg377Arg
M0115044 PNLAMIBE_00276 198881 3 Skin 0.05 protein_coding synonymous_variant LOW 1140G>T Val380Val
M0115045 PNLAMIBE_00276 198900 3 Skin 0.05 protein_coding missense_variant MODERATE 1159G>A Ala387Thr
M0115046 PNLAMIBE_00276 198902 3 Skin 0.05 protein_coding synonymous_variant LOW 1161T>C Ala387Ala
M0115047 PNLAMIBE_00276 198923 3 Skin 0.05 protein_coding synonymous_variant LOW 1182T>C Phe394Phe
M0115048 PNLAMIBE_00276 198930 3 Skin 0.05 protein_coding missense_variant MODERATE 1189A>G Ile397Val
M0115049 PNLAMIBE_00276 198933 3 Skin 0.05 protein_coding missense_variant MODERATE 1192A>C Ile398Leu
M0115050 PNLAMIBE_00276 198944 3 Skin 0.05 protein_coding synonymous_variant LOW 1203G>C Thr401Thr
M0115051 PNLAMIBE_00276 198956 3 Skin 0.05 protein_coding synonymous_variant LOW 1215C>T Thr405Thr
M0115052 PNLAMIBE_00276 199148 5 Skin 0.08 protein_coding synonymous_variant LOW 1407A>C Leu469Leu
M0115053 PNLAMIBE_00276 199178 5 Skin 0.08 protein_coding synonymous_variant LOW 1437A>G Leu479Leu
M0115054 PNLAMIBE_00277 199549 3 Skin 0.05 protein_coding synonymous_variant LOW 123C>A Arg41Arg
M0115055 PNLAMIBE_00277 199552 3 Skin 0.05 protein_coding synonymous_variant LOW 126G>A Ala42Ala
M0115056 PNLAMIBE_00277 199586 3 Skin 0.05 protein_coding missense_variant MODERATE 160G>A Ala54Thr
M0115057 PNLAMIBE_00278 200739 3 Skin 0.05 protein_coding synonymous_variant LOW 408A>C Leu136Leu
M0115058 PNLAMIBE_00281 202846 3 Skin 0.05 protein_coding synonymous_variant LOW 30C>T Ala10Ala
M0115059 PNLAMIBE_00281 202861 3 Skin 0.05 protein_coding synonymous_variant LOW 15C>G Thr5Thr
M0115060 PNLAMIBE_00281 202871 3 Skin 0.05 protein_coding missense_variant MODERATE 5G>A Ser2Asn
M0115061 PNLAMIBE_00280 202880 3 Skin 0.05 protein_coding upstream_gene_variant MODIFIER -367T>G None
M0115062 PNLAMIBE_00282 202893 3 Skin 0.05 protein_coding splice_region_variant&stop_retained_variant LOW 635A>G Ter212Ter
M0115063 PNLAMIBE_00282 202895 3 Skin 0.05 protein_coding synonymous_variant LOW 633A>G Gly211Gly
M0115064 PNLAMIBE_00282 202898 3 Skin 0.05 protein_coding synonymous_variant LOW 630T>C Ala210Ala
M0115065 PNLAMIBE_00282 202922 3 Skin 0.05 protein_coding synonymous_variant LOW 606C>T Asp202Asp
M0115066 PNLAMIBE_00282 202946 3 Skin 0.05 protein_coding synonymous_variant LOW 582T>C Leu194Leu
M0115067 PNLAMIBE_00276 198620 3 Skin 0.05 protein_coding synonymous_variant LOW 879C>T Leu293Leu
M0115068 PNLAMIBE_00276 199366 3 Skin 0.05 protein_coding missense_variant MODERATE 1625A>G Asp542Gly
M0115069 PNLAMIBE_00329 243523 3 Skin 0.05 protein_coding missense_variant MODERATE 162A>C Leu54Phe
M0115070 PNLAMIBE_00276 199160 3 Skin 0.05 protein_coding synonymous_variant LOW 1419G>A Arg473Arg
M0115071 PNLAMIBE_00276 199211 3 Skin 0.05 protein_coding synonymous_variant LOW 1470A>G Ser490Ser
M0115072 PNLAMIBE_00276 199215 3 Skin 0.05 protein_coding synonymous_variant LOW 1474C>T Leu492Leu
M0115073 PNLAMIBE_00276 199241 3 Skin 0.05 protein_coding synonymous_variant LOW 1500A>C Arg500Arg
M0115074 PNLAMIBE_00276 199250 3 Skin 0.05 protein_coding synonymous_variant LOW 1509G>T Val503Val
M0115075 PNLAMIBE_00276 199265 3 Skin 0.05 protein_coding synonymous_variant LOW 1524A>G Lys508Lys






Analysis of virulence factors contributing to bacterial pathogenicity


This table presents virulence factors identified within the plasmid cluster.
      Note: Virulence factor analysis was performed using VFDB. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known virulence factors are listed.

Gene Name vf_gene_id vf_name identity evalue qstart qend query_coverage subject_coverage vf_category gene_description condition







        Analysis of biocide and heavy metal resistance genes to assess antimicrobial risk and environmental impact


This table presents biocides and heavy metals resistance genes identified within the plasmid cluster.
      Note: Analyzing biocide and heavy metal resistance genes based on BacMet to evaluate bacterial resistance risk and the potential impact of environmental heavy metal contamination. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, E-value < 1e-5) to known biocide and heavy metal resistance genes are listed.

Gene Name compound identity evalue qstart qend query_coverage subject_coverage group
PNLAMIBE_00246 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Pyronin Y [class: Xanthene], Rhodamine 6G [class: Xanthene], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Acridine Orange [class: Acridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Sodium Deoxycholate (SDC) [class: Acid], Crystal Violet [class: Triarylmethane], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)] 100 1.1e-60 1 115 1.0000 1.0000 experiment
PNLAMIBE_00258 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Pyronin Y [class: Xanthene], Rhodamine 6G [class: Xanthene], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Acridine Orange [class: Acridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Sodium Deoxycholate (SDC) [class: Acid], Crystal Violet [class: Triarylmethane], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)] 100 1.1e-60 1 115 1.0000 1.0000 experiment
PNLAMIBE_00280 Mercury (Hg) 100 2.9e-41 1 78 1.0000 1.0000 experiment
PNLAMIBE_00281 Mercury (Hg) 98.3 1.6e-62 1 121 1.0000 1.0000 experiment
PNLAMIBE_00356 Antimony (Sb), Arsenic (As), Glycerol [class: Alcohol] 72.4 6.6e-112 6 273 0.9571 0.9537 experiment
PNLAMIBE_00442 Tellurium (Te) 70.7 5.6e-78 1 191 0.9948 1.0000 experiment
PNLAMIBE_00443 Tellurium (Te) 70.3 3.6e-77 1 192 1.0000 1.0000 experiment
PNLAMIBE_00444 Tellurium (Te) 71.3 2.9e-138 1 340 0.9942 0.9884 experiment
PNLAMIBE_00280 Mercury (Hg) 100 6.6e-39 1 78 1.0000 1.0000 prediction
PNLAMIBE_00281 Mercury (Hg) 100 7.3e-61 1 121 1.0000 1.0000 prediction
PNLAMIBE_00328 Mercury (Hg) 96.7 9.7e-42 1 91 1.0000 1.0000 prediction
PNLAMIBE_00356 Antimony (Sb), Arsenic (As), Glycerol [class: Alcohol] 72.3 1.2e-111 9 279 0.9679 0.9576 prediction
PNLAMIBE_00442 Tellurium (Te) 71.2 5.7e-76 1 191 0.9948 1.0000 prediction
PNLAMIBE_00443 Tellurium (Te) 72.4 1e-77 1 192 1.0000 1.0000 prediction
PNLAMIBE_00444 Tellurium (Te) 72.2 5e-139 1 340 0.9942 0.9884 prediction
PNLAMIBE_00633 Arsenic (As) 94.7 3.7e-159 9 290 0.9658 0.7877 prediction






        Analyzing antimicrobial resistance genes to assess bacterial resistance to antibiotics and other antimicrobial agents


This table presents antimicrobial resistance genes identified within the plasmid cluster.
      Note: Antimicrobial resistance was performed using CARD. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known antimicrobial resistance genes are listed.

Gene Name aro_accession identity evalue qstart qend query_coverage subject_coverage drug_class amr_gene_family resistance_mechanism
PNLAMIBE_00232 ARO:3003071 100 5.01e-226 1 299 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
PNLAMIBE_00237 ARO:3003109 100 0 1 491 1.0000 1.0000 macrolide antibiotic msr-type ABC-F protein antibiotic target protection
PNLAMIBE_00238 ARO:3003741 100 1.87e-214 1 294 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
PNLAMIBE_00241 ARO:3002594 100 2.6e-139 1 184 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
PNLAMIBE_00242 ARO:3004665 100 4.51e-301 1 419 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
PNLAMIBE_00243 ARO:3001807 100 1.22e-191 52 317 0.8391 1.0000 cephalosporin OXA beta-lactamase antibiotic inactivation
PNLAMIBE_00244 ARO:3002848 100 4.06e-115 1 150 1.0000 1.0000 rifamycin antibiotic rifampin ADP-ribosyltransferase (Arr) antibiotic inactivation
PNLAMIBE_00245 ARO:3004550 100 9.81e-115 1 157 1.0000 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement
PNLAMIBE_00246 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
PNLAMIBE_00247 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
PNLAMIBE_00251 ARO:3006890 100 1.25e-194 1 267 1.0000 1.0000 carbapenem AFM beta-lactamase antibiotic inactivation
PNLAMIBE_00252 ARO:3001205 97.5 2.28e-89 1 121 1.0000 1.0000 glycopeptide antibiotic Bleomycin resistant protein antibiotic inactivation
PNLAMIBE_00255 ARO:3004635 100 2.96e-109 1 152 1.0000 1.0000 aminoglycoside antibiotic AAC(6') antibiotic inactivation
PNLAMIBE_00256 ARO:3000230 100 5.85e-134 41 217 0.8157 1.0000 aminoglycoside antibiotic ANT(2'') antibiotic inactivation
PNLAMIBE_00257 ARO:3002695 99 3.55e-298 1 419 1.0000 1.0000 phenicol antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
PNLAMIBE_00258 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
PNLAMIBE_00259 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
PNLAMIBE_00262 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
PNLAMIBE_00266 ARO:3002799 100 1.34e-79 1 218 1.0000 1.0000 fluoroquinolone antibiotic quinolone resistance protein (qnr) antibiotic target protection
PNLAMIBE_00267 ARO:3004660 99.5 2.09e-160 1 210 1.0000 1.0000 phenicol antibiotic chloramphenicol acetyltransferase (CAT) antibiotic inactivation
PNLAMIBE_00268 ARO:3002243 99.7 4.71e-205 1 288 1.0000 1.0000 penicillin beta-lactam CARB beta-lactamase antibiotic inactivation






Analysis of pathogenicity genes to explore pathogen-host interactions


This table presents host pathogen-host interactions within the plasmid cluster.
      Note: Analyzing pathogenicity-related genes using PHI-base to understand pathogen virulence mechanisms and their impact on host interactions. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e-5) to known pathogenicity-related genes are listed.

Gene Name phi_molconn_id host gene_name identity evalue qstart qend query_coverage subject_coverage host_descripton disease_name function phenotype_of_mutant
PNLAMIBE_00016 PHI:7131 greB 71.6 6.9e-60 1 155 0.9281 0.9873 rodents salmonellosis transcription elongation factor loss of pathogenicity
PNLAMIBE_00240 PHI:9804 int 100 3.8e-14 1 37 0.1160 1.0000 rodents gastroenteritis integrase reduced virulence
PNLAMIBE_00251 PHI:6347 NDM-1 86.6 2.2e-132 7 267 0.9775 0.9667 moths infection carbapenemase unaffected pathogenicity
PNLAMIBE_00254 PHI:9804 int 100 3.3e-14 1 37 0.1317 1.0000 rodents gastroenteritis integrase reduced virulence
PNLAMIBE_00304 PHI:3165 hopA1 82.3 1.1e-144 39 331 0.8852 1.0000 eudicots leaf spot (celery); leaf spot (eggplant); leaf spot (sweet pepper); wilt rot (muskmelon); stem rot (muskmelon); stem rot (chrysanthemum); leaf spot (soybean) effector (plant avirulence determinant) effector (plant avirulence determinant)
PNLAMIBE_00551 PHI:10380 RecA 73.2 1.1e-139 1 328 0.9507 0.9398 nematodes nosocomial infection DNA strand exchange and recombination protein reduced virulence






        Analyzing carbohydrate-active enzyme genes to uncover mechanisms of nutrient degradation


This table presents carbohydrate-active enzyme genes identified within the plasmid cluster.
      Note: Annotation of carbohydrate-active enzyme genes was performed using CAZy to explore mechanisms of nutrient breakdown and utilization. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known CAZyme genes are listed.

Gene Name cazy_id identity evalue qstart qend query_coverage subject_coverage
PNLAMIBE_00022 UUC21733.1|GT2 97.1 3.17e-192 1 273 1 1
PNLAMIBE_00190 QFX78706.1|GH23 100 9.1e-168 1 234 1 1





        Analyzing transport proteins to understand bacterial strategies for substrate uptake and detoxification


This table presents transport proteins within the plasmid cluster.
      Note: Investigation of transport proteins based on TCDB to uncover bacterial mechanisms of substrate transport and environmental detoxification. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known transport protein entries are listed.

Gene Name tcid identity evalue qstart qend query_coverage subject_coverage class_field class_term subclass subclass_term family family_term
PNLAMIBE_00242 2.A.1.2.3 96.4 6.9e-226 1 419 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
PNLAMIBE_00257 2.A.1.2.3 98.8 1.2e-230 1 419 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
PNLAMIBE_00280 1.A.72.5.1 78.2 1.1e-31 1 78 1.0000 1.0000 1 Channels/Pores 1.A α-Type Channels 1.A.72 The Mercuric Ion Pore (Mer) Superfamily
PNLAMIBE_00356 1.A.8.1.1 72.4 2.5e-110 6 273 0.9571 0.9537 1 Channels/Pores 1.A α-Type Channels 1.A.8 The Major Intrinsic Protein (MIP) Family
PNLAMIBE_00444 2.A.109.1.1 71.9 1.8e-139 1 340 0.9884 0.9884 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.109 The Tellurium Ion Resistance (TerC) Family